Liquid Biopsy of Cerebrospinal Fluid Enables Selective Profiling of Glioma Molecular Subtypes at First Clinical Presentation

Abstract

Purpose: Current glioma diagnostic guidelines call for molecular profiling to stratify patients into prognostic and treatment subgroups. In case the tumor tissue is inaccessible, cerebrospinal fluid (CSF) has been proposed as a reliable tumor DNA source for liquid biopsy. We prospectively investigated the use of CSF for molecular characterization of newly diagnosed gliomas. Experimental design: We recruited two cohorts of newly diagnosed glioma patients, one (n=45) providing CSF collected in proximity of the tumor, the other (n=39) CSF collected by lumbar puncture. Both cohorts provided tumor tissues by surgery concomitant with CSF sampling. DNA samples retrieved from CSF and matched tumors were systematically characterized and compared by comprehensive (NGS) or targeted (ddPCR) methodologies. Conventional and molecular diagnosis outcomes were compared. Results: We report that tumor DNA is abundant in CSF close to the tumor, but scanty and mostly below NGS sensitivity threshold in CSF from lumbar puncture. Indeed, tumor DNA is 15 mostly released by cells invading liquoral spaces, generating a gradient that attenuates by departing from the tumor. Nevertheless, in >60% of lumbar puncture CSF samples, tumor DNA is sufficient to assess a selected panel of genetic alterations (IDH and TERT promoter mutations, EGFR amplification, CDKN2A/B deletion: ITEC protocol) and MGMT methylation that, combined with imaging, enable tissue-agnostic identification of main glioma molecular subtypes. Conclusions: This study shows potentialities and limitations of CSF liquid biopsy in achieving molecular characterization of gliomas at first clinical presentation and proposes a protocol to maximize diagnostic information retrievable from CSF DNA.

Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid

“…This highly sensitive technique successfully detected ctDNA targeting H3 K27M and pTERT mutations in gliomas [ 56 , 76 , 83 , 98 , 99 ]. Table 1 summarizes the representative studies utilizing digital PCR on CSF and shows that digital PCR can detect variant alleles with a high sensitivity of 70–100% in glioblastoma and 80–100% in DMG [ 13 , 56 , 76 , 83 , 92 , 93 , 100 ]. However, even with digital PCR using CSF, the detection of low-grade gliomas is challenging, as they are generally detected in less than 50% of cases, and in some cases, they are not identified at all.…”

Beyond blood: Advancing the frontiers of liquid biopsy in oncology and personalized medicine

“…These findings are particularly crucial for patients with tumors in locations inaccessible to surgical biopsy or those who cannot undergo such procedures due to medical comorbidities. 76 However, the application of CSF-based liquid biopsies in clinical practice is at a nascent stage, with several challenges that need addressing. The invasiveness of CSF collection, typically through lumbar puncture, poses risks and could limit the frequency of sampling.…”

“…For example, studies have reported the successful identification of key mutations in CSF from glioma patients, providing actionable insights into tumor genomics. These findings are particularly crucial for patients with tumors in locations inaccessible to surgical biopsy or those who cannot undergo such procedures due to medical comorbidities 76 …”

“…These findings are particularly crucial for patients with tumors in locations inaccessible to surgical biopsy or those who cannot undergo such procedures due to medical comorbidities. 76 …”

A Clinical Audit: Assessing the Diagnostic Delay of Primary Brain Tumors, Glioblastoma IDH-Wild Type and Primary CNS Lymphoma; Exploring the Use of CSF Liquid Biopsy

“…Sensitive and molecular assays enable enhancements and higher detectable rates. [85] CSF Diagnostic yield may be improved by identification of Clonal IGH rearrangements. This refers to specific rearrangements of immunoglobulin heavy chain gene, they are produced by B-cells.…”